Thermo-Flux

Thermo-Flux converts stoichiometric metabolic network models into comprehensive thermodynamic-stoichiometric models to improve flux predictions in metabolic modeling and flux balance analysis (FBA).

Key Features:

• Automated Mass and Charge Balancing: Automates mass and charge balancing while considering physical and biochemical parameters.
• Transporter Variant Definition: Enables definition of transporter variants and Gibbs energies for membrane transport.
• Handling of Unknown Metabolites: Provides robust handling of metabolites with unknown structures or Gibbs energies.
• Integration of Gibbs Energy Advances: Integrates recent advances in determining Gibbs energies and their respective uncertainties.

Scientific Applications:

• Metabolic Research: Supports fundamental metabolic research by converting stoichiometric models into thermodynamic-stoichiometric models for improved analysis.
• Biotechnological Applications: Enables biotechnological applications through improved flux predictions in genome-scale metabolic models.
• Database Model Conversion: Converts stoichiometric models from the BiGG database into comprehensive thermodynamic-stoichiometric models.
• Genome-Scale Model Analysis: Improves flux predictions for genome-scale models such as the yeast model iMM904.

Methodology:

Thermo-Flux uses a semi-automated pipeline to convert stoichiometric metabolic network models into thermodynamic-stoichiometric models, incorporating thermodynamic constraints, transporter variants, and recent advances in Gibbs energy determination with uncertainties.